9G0T | pdb_00009g0t

Xenopus tropicalis undecorated microtubule - 15 protofilament, 3-start helix

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other

Sample
Undecorated tubulin lattice following polymerisation with GTP (no stabilising ligands).

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	The sample was incubated on the grid for 10 minutes within the Leica chamber to allow for tubulin polymerisation.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	486937
Reported Resolution (Å)	3.5
Resolution Method	FSC 0.143 CUT-OFF
Other Details	These are pseudo-particles following the symmetry expansion of ~46,000 particles
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Initially a tubulin dimer was docked into the density within ChimeraX, then molecular dynamics force field-based model fitting was carried out by ISOL ...	Initially a tubulin dimer was docked into the density within ChimeraX, then molecular dynamics force field-based model fitting was carried out by ISOLDE using unsharpened and deepEMhancer processed density. The model was refined through iterations of ISOLDE and Phenix real_space_refinement softwares.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	600
Maximum Defocus (nm)	2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	v1.7.6.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	CTFFIND	4
MODEL FITTING	ISOLDE
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		192000

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.